Hello Brigitte, The best place to find source information to address your questions is in the track descriptions themselves. Both have methods and links to the 3rd party datasets and tools used to generate the annotation.
In particular, when reviewing each, please note: for the RepeatMasker track: the program RepeatMasker was used. Several repeat libraries are available for use with this program, including those in the category "simple repeat". for the Microsatellites track: the program Tandem Repeats Finder was used. The annotation in this track is also considered in the category of a "simple repeat" as noted in the methods. Click out to the external documentation for details, links to publications, and explanations of the biology behind each method. For your case, the two annotation methods are both identifying basically the same feature in your region of interest. Difference are most likely related to the distinct methods used rather than any large difference in how to interpret the result. Which is better or more correct or contained in your actual amplified sample is something that you will need to determine (keeping in mind that repeat libraries often represent generalizations - you sample is a real, distinct, and possibly variant example of the generalized annotation contained in the Browser tracks). Review the annotation feature descriptions and this will become more clear. Good luck with your research, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Birgitte Bertelsen" <[email protected]> wrote: > From: "Birgitte Bertelsen" <[email protected]> > To: [email protected] > Sent: Saturday, January 9, 2010 11:28:33 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Variation of simple tandem repeats and microsattelites > > Hi > > I have a question regarding the "variation and repeats" option when > using the hg18 version of the Genome browser. > > I have found two repeats within the region: > chrX:48,578,098-48,578,437. One of them is a AG repeat listed as a > Simple tandem repeat while the other is a CA repeat listed as both a > simple tandem repeat and a microsattelite. What is the difference > between these two repeat definitions? And more importantly does both > of them vary in number of repeat units, and how can I see which one. I > have aplified this region and obtained fragments of different lengths > but I am unsure which of the repeats giving rise to the observed > variation. > > Thanks > > Birgitte > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
